Functional Genomics of <i>ABCA3</i> Variants

Abstract

Rare or private, biallelic variants in the <i>ABCA3</i> (ATP-binding cassette transporter A3) gene are the most common monogenic cause of lethal neonatal respiratory failure and childhood interstitial lung disease. Functional characterization of fewer than 10% of over 200 disease-associated <i>ABCA3</i> variants (majority missense) suggests either disruption of ABCA3 protein trafficking (type I) or of ATPase-mediated phospholipid transport (type II). Therapies remain limited and nonspecific. A scalable platform is required for functional characterization of <i>ABCA3</i> variants and discovery of pharmacologic correctors. To address this need, we first silenced the endogenous <i>ABCA3</i> locus in A549 cells with CRISPR/Cas9 genome editing. Next, to generate a parent cell line (A549/<i>ABCA3</i>^<i>-/-</i>) with a single recombination target site for genomic integration and stable expression of individual <i>ABCA3</i> missense variant cDNAs, we used lentiviral-mediated integration of a LoxFAS cassette, FACS, and dilutional cloning. To assess the fidelity of this cell-based model, we compared functional characterization (ABCA3 protein processing, ABCA3 immunofluorescence colocalization with intracellular markers, ultrastructural vesicle phenotype) of two individual ABCA3 mutants (type I mutant, p.L101P; type II mutant, p.E292V) in A549/<i>ABCA3</i>^<i>-/-</i> cells and in both A549 cells and primary, human alveolar type II cells that transiently express each cDNA after adenoviral-mediated transduction. We also confirmed pharmacologic rescue of <i>ABCA3</i> variant-encoded mistrafficking and vesicle diameter in A549/<i>ABCA3</i>^<i>-/-</i> cells that express p.G1421R (type I mutant). A549/<i>ABCA3</i>^<i>-/-</i> cells provide a scalable, genetically versatile, physiologically relevant functional genomics platform for discovery of variant-specific mechanisms that disrupt ABCA3 function and for screening of potential ABCA3 pharmacologic correctors.